Software Resources

When a researcher is first confronted with a problem, the first step is to look at the available solutions. Below is a list of freely available tools for medical image processing and computer-aided surgery.

VTK is an open-source software toolkit for visualization, computer graphics, and image processing with a great online community and numerous examples. VTK is cross platform with implementations for Windows, Mac OS, Unix, and Linux. Users can code in C++, Java, Python, or TCL. Knowledge of VTK means that developers can take advantage of other tools such as ITK, ITK-SNAP, IGSTK, and 3D Slicer, to name a few. VTK_150_RO
ITK is an open-source, cross-platform system that sits on top of VTK. It provides developers with an extensive suite of software tools for image analysis.  ITK_150_RO
IGSTK is a framework that provides a common functionality for image-guided surgery applications. IGSTK makes easy work of communicating with hardware interfaces such as Northern Digital tracking systems, creating a simple navigational display, and reading of medical images. igstk_150_RO
ITK-SNAP is a freely available tool built on ITK and VTK for image manipulation. The source code for ITK-SNAP is part of ITK Applications, so developers can add their own modifications. snaplogo3
MITK is an open-source toolkit for medical imaging that provides functionality beyond ITK and VTK. mitklogo
OpenCV is free for both academic and commercial use with C++, C, Python and Java interfaces and support for Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Usage ranges from standard computer vision algorithms to advanced robotics with a large user base. opencv_logo
ImageJ is a cross platform tool for medical image manipulation, including basic utilities such as resampling. ImageJ is very good for reading in medical images in dicom format. imagej-logo
3D Slicer is cross platform, open source software package for visualization and image analysis. Slicer_150_RO
Osirix is a Mac OS only application for sophisticated rendering and manipulation of medical image data. Osirix is particularly useful for interpreting any kind of dicom image.  osirix_logo
DCMTK is a collection of libraries and applications for reading, writing, and otherwise manipulating dicom images. It works with multiple operating systems and is easy to install. I used it to build my own dicom anonymization interface. dcmtklogo
Paraview is a cross platform, freely available application for visualization. Users can create quickly create scenes with 3D data for interpretation and analysis. Paraview is based on VTK so it supports VTK objects. ParaView_150_RO
CMake is a cross platform application that manages the compile process. It automatically generates Makefiles (Linux, Unix, Mac OS) and projects (Windows) for your code base. CMake_150_RO
MeshLab is an open source system for the processing and editing of unstructured 3D triangular meshes. MeshLab is great for clipping and cleaning up meshes. VTK polydata can be converted to MeshLab objects and vice versa.  meshlab
FreeSurfer is an open source software application for processing and analyzing brain MRI images. Tools include registration, longitudinal analysis, segmentation, and reconstruction.  freesurfer_logo

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